RESUMO
From the database point of view, biomolecular pathways are sets of proteins and other biomacromolecules that represent spatio-temporally organized cascades of interactions with the involvement of low-molecular compounds and are responsible for achieving specific phenotypic biological outcomes. A pathway is usually associated with certain subcellular compartments. In this chapter, we analyze the major public biomolecular pathway databases. Special attention is paid to database scope, completeness, issues of annotation reliability, and pathway classification. In addition, systems for information retrieval, tools for mapping user-defined gene sets onto the information in pathway databases, and their typical research applications are reviewed. Whereas today, pathway databases contain almost exclusively qualitative information, the desired trend is toward quantitative description of interactions and reactions in pathways, which will gradually enable predictive modeling and transform the pathway databases into analytical workbenches.
Assuntos
Mineração de Dados , Bases de Dados Genéticas , Bases de Dados de Proteínas , Redes e Vias Metabólicas , Proteínas/metabolismo , Biologia de Sistemas , Animais , Humanos , Disseminação de Informação , Internet , Redes e Vias Metabólicas/genética , Proteínas/genética , Software , Integração de Sistemas , Terminologia como AssuntoRESUMO
In the current understanding, translation of genomic sequences into proteins is the most important path for realization of genome information. In exercising their intended function, proteins work together through various forms of direct (physical) or indirect interaction mechanisms. For a variety of basic functions, many proteins form a large complex representing a molecular machine or a macromolecular super-structural building block. After several high-throughput techniques for detection of protein-protein interactions had matured, protein interaction data became available in a large scale and curated databases for protein-protein interactions (PPIs) are a new necessity for efficient research. Here, their scope, annotation quality, and retrieval tools are reviewed. In addition, attention is paid to portals that provide unified access to a variety of such databases with added annotation value.
Assuntos
Mineração de Dados , Bases de Dados de Proteínas , Domínios e Motivos de Interação entre Proteínas , Mapeamento de Interação de Proteínas , Proteínas/química , Biologia de Sistemas , Animais , Humanos , Internet , Complexos Multiproteicos , Software , Integração de Sistemas , Terminologia como AssuntoRESUMO
The Gastric Cancer (Biomarkers) Knowledgebase (GCBKB) (http://biomarkers.bii.a-star.edu.sg/background/gastricCancerBiomarkersKb.php) is a curated and fully integrated knowledgebase that provides data relating to putative biomarkers that may be used in the diagnosis and prognosis of gastric cancer. It is freely available to all users. The data contained in the knowledgebase was derived from a large literature source and the putative biomarkers therein have been annotated with data from the public domain. The knowledgebase is maintained by a curation team who update the data from a defined source. As well as mining data from the literature, the knowledgebase will also be populated with unpublished experimental data from investigators working in the gastric cancer biomarker discovery field. Users can perform searches to identify potential markers defined by experiment type, tissue type and disease state. Search results may be saved, manipulated and retrieved at a later date. As far as the authors are aware this is the first open access database dedicated to the discovery and investigation of gastric cancer biomarkers.
